Studies in adult mild traumatic brain injury (mTBI) have shown that two key measures of attention, spatial reorienting and inhibition of return (IOR), are impaired during the first few weeks of injury. However, it is currently unknown whether similar deficits exist following pediatric mTBI. The current study used fMRI to investigate the effects of semi-acute mTBI (< 3 weeks post-injury) on auditory orienting in 14 pediatric mTBI patients (age 13.50 ± 1.83; education: 6.86 ± 1.88) and 14 healthy controls (age 13.29 ± 2.09; education: 7.21 ± 2.08) matched for age and years of education. Results indicated that patients with mTBI showed subtle (i.e., moderate effect sizes) but non-significant deficits on formal neuropsychological testing and during inhibition of return. In contrast, functional imaging results indicated that patients with mTBI demonstrated significantly decreased activation within the bilateral posterior cingulate gyrus, thalamus, basal ganglia, midbrain nuclei, and cerebellum. The spatial topography of hypoactivation was very similar to our previous study in adults, suggesting that subcortical structures may be particularly affected by the initial biomechanical forces in mTBI. Current results also suggest that fMRI may be a more sensitive tool for identifying semi-acute effects of mTBI than the procedures currently used in clinical practice such as neuropsychological testing and structural scans. fMRI findings could potentially serve as a biomarker for measuring the subtle injury caused by mTBI and documenting the course of recovery.